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Coffee and Your Gut Microbiome: What the Study Actually Found (vs. the Headlines)

  • Writer: Joyce Knieff, ND, LAc
    Joyce Knieff, ND, LAc
  • Aug 13
  • 4 min read

Coffee headlines follow a pattern: a new study comes out, and within a week it's either "coffee will save your brain" or "coffee is secretly wrecking you." A widely covered new study out of University College Cork's APC Microbiome Ireland gives us a good chance to slow down and look at what the researchers actually reported, not just what the press release promised.


A white cup of brewed coffee surrounded by roasted coffee beans
Photo: john renzzel / Unsplash

What the research found


The study compared 31 regular coffee drinkers (3 to 5 cups a day) with 31 non-coffee drinkers, then had the coffee drinkers stop for two weeks before reintroducing either caffeinated or decaffeinated coffee, without anyone knowing which they'd gotten. Researchers tracked gut microbiome composition, metabolites, and psychological measures throughout [1].


Coffee drinkers showed higher levels of two bacterial species, Cryptobacterium and Eggerthella, along with lower levels of a couple of gut metabolites and of GABA, a calming neurotransmitter also produced in the gut [1]. Some of these changes reversed during the two-week break and shifted again once coffee was reintroduced, and that shift happened regardless of whether the coffee had caffeine in it, so at least part of what's going on here isn't about caffeine alone.


The peer-reviewed findings are more complicated than the headlines suggested. Coffee drinkers in this study actually showed greater impulsivity and emotional reactivity, and the non-coffee drinkers performed better on memory tests, not the other way around [1]. Press coverage of this same study, including the university's own release, emphasized improved mood and reduced stress across both coffee groups and better memory specifically with decaf. That's a real gap between the press framing and what the peer-reviewed abstract itself reports, and it's a good reminder to read past the press release before deciding what a study found.


The bigger picture


Coffee's relationship with the gut microbiome is actually one of the more consistently replicated findings in nutrition science, even if the mood and cognition piece is messier. A 2024 analysis of over 54,000 people across 211 cohorts found that coffee drinking reliably predicted higher levels of a specific gut bacterium, Lawsonibacter asaccharolyticus, regardless of country or population [2]. Separately, a 2025 analysis of continuous glucose monitors in nearly 8,700 adults found habitual coffee intake tracked with more favorable blood sugar regulation, and gut microbial composition was one of the biological systems most closely tied to coffee intake [3].


Dose seems to matter here too. A 2024 review found moderate coffee intake, under about four cups a day, tends to favor bacteria generally considered beneficial, while intake above five cups a day has been linked to reflux, gum disease, and worse outcomes in Crohn's disease [4]. So "coffee affects your gut microbiome" is well supported. "Coffee makes everyone calmer and sharper" is not quite what this particular study showed.


The naturopathic lens


I don't think in terms of coffee being universally good or universally bad, because that's not how any single food or habit actually behaves in a body. What this study is really describing is individual variation: the same cup of coffee nudges gut bacteria, neurotransmitter production, and mood-related behavior in ways that differ from person to person and possibly from gut to gut.


That variation is exactly why I ask patients with anxiety, reflux, sleep trouble, or SIBO to pay close attention to their own response to coffee rather than defaulting to whatever the latest headline says. Some people's nervous systems handle caffeine well within a broader pattern of good sleep and low stress. Others find that coffee amplifies the same jitteriness or reactivity this study picked up on, especially when the adrenal and gut-brain systems are already under strain. Neither response is "wrong." They're just different terrain.


So how does this translate to life?


A coffee habit that feels good and isn't interfering with sleep, anxiety, or digestion doesn't need to change on account of this study. If you've been wondering whether coffee is part of why you feel anxious, wired, or reflux-prone, a genuine two-to-four week trial off it, the same kind of break this study used, can tell you more about your own body than any population-level finding. Pay attention to mood, sleep quality, and digestion during that window, and loop your care team in if you're making a bigger change, especially if caffeine is tangled up with a medication or a condition like anxiety, insomnia, or reflux.


References


  1. Boscaini S, et al. Habitual coffee intake shapes the gut microbiome and modifies host physiology and cognition. Nature Communications. 2026;17(1). doi: 10.1038/s41467-026-71264-8

  2. Manghi P, et al. Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts. Nature Microbiology. 2024.

  3. Dai J, et al. Phenome-wide associations of coffee intake in the human phenotype project. Metabolism: Clinical and Experimental. 2025.

  4. Saygili S, et al. Effects of Coffee on Gut Microbiota and Bowel Functions in Health and Diseases: A Literature Review. Nutrients. 2024.

  5. Original article: "Coffee, the Microbiome & Metabolic Health: What a New Nature Study Reveals." Today's Practitioner, 2026. https://todayspractitioner.com/microbiome/coffee-the-microbiome-metabolic-health-what-a-new-nature-study-reveals/ (secondary coverage; primary study cited above is the main reference for this piece)


Disclaimer


This article is for general educational purposes only and is not a substitute for individualized medical advice, diagnosis, or treatment. Always talk with your own healthcare provider about any symptoms, medications, or changes to your care.



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The kind of trial described above only tells you something if you write it down as you go. A dated daily log with space for food, mood, sleep, and digestion keeps a two-to-four week experiment readable afterward instead of leaving you to reconstruct it from memory.




If this resonates with what you're experiencing and you'd like to explore a naturopathic approach, book a consultation with our clinic.




 
 
 

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